I'm also having a hard time with playing this as a backup copy. Ripped it myself, altered the main.dol, reinserted and scrubbed it. NeoGamma recognizes it, but I get stuck on a green screen. I'm on 4.2U safely through hax, just updated to r15 and I'm still stuck. At least I can past the time figuring this out by playing the game...

Where did I go wrong? What can I do to fix it? Does GX support alt-dol's? How does that work?

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If you don't know that it supports alt dols then I know why you can't make it work. You never bothered trying to config the game. You need to set 002 fix to ON and (i forgot if this was usbloader or usbloader gx) change the IOS to 249.